SELECT COUNT(DISTINCT seq) FROM Peptide;
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EXPLAIN AND DESCRIBE:
mysql> explain select count(distinct seq) from Peptide;
+---------+------+---------------+------+---------+------+---------+--
+-----+
| table   | type | possible_keys | key  | key_len | ref  | rows    | E
+xtra |
+---------+------+---------------+------+---------+------+---------+--
+-----+
| Peptide | ALL  | NULL          | NULL |    NULL | NULL | 1860342 |  
+     |
+---------+------+---------------+------+---------+------+---------+--
+-----+
1 row in set (0.02 sec)

mysql> desc Peptide;
+--------+---------------------------+------+-----+------------+------
+----------+
| Field  | Type                      | Null | Key | Default    | Extra
+          |
+--------+---------------------------+------+-----+------------+------
+----------+
| pepid  | int(10) unsigned zerofill |      | PRI | NULL       | auto_
+increment |
| proid  | int(10) unsigned zerofill |      | MUL | 0000000000 |      
+          |
| seq    | tinytext                  |      | MUL |            |      
+          |
| mh     | double                    |      |     | 0          |      
+          |
| expect | double                    |      |     | 0          |      
+          |
| start  | int(11)                   |      |     | 0          |      
+          |
| end    | int(11)                   |      |     | 0          |      
+          |
| charge | tinyint(1) unsigned       | YES  |     | NULL       |      
+          |
| delta  | float                     |      |     | 0          |      
+          |
| dida   | int(11)                   |      |     | 0          |      
+          |
| didb   | int(11)                   |      |     | 0          |      
+          |
| didc   | int(11)                   |      |     | 0          |      
+          |
+--------+---------------------------+------+-----+------------+------
+----------+
12 rows in set (0.00 sec)
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C:\testing\scripts>perl stat_tester.pl
Connected
DBD::mysql::db do failed: Lost connection to MySQL server during query
+ at stat_tester.pl line 54.
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I doubt that it is a problem with DBI/DBD::mysql, mainly because DBD::mysql is reporting that the server closed the connection. It sounds like somesort of timeout, too large of a packect, commands being sent out of order, or something else that causes the server to go away (segfault is a possibility too).

You might want to enable tracing on the serverside, to see why the connection is going away.

You can try also the DBD::mysql mailing list

Here is the MySQL developers section on this http://dev.mysql.com/doc/mysql/en/Gone_away.html

Anyway the query will take a long time as it needs a full table scan*. You must have a slow server/disks as it takes me 1.67 seconds to run a similar query on a million row data set. As noted by astroboy forking can cause this issue, but I suspect it is something to do with your MySQL configuration. Here is what we use with 2GB of RAM. It might be worth a try. The extended timeouts discussed before are not included (never needed them) but should be. There is some suggestion the connect timeout you can set here may be important.

[mysqld]
datadir=/var/lib/mysql
socket=/tmp/mysql.sock
set-variable=wait_timeout=200000
set-variable=key_buffer=256M
set-variable=max_allowed_packet=32M
set-variable=table_cache=512
set-variable=sort_buffer_size=64M
set-variable=record_buffer=64M
set-variable=read_buffer_size=32M
set-variable=myisam_sort_buffer_size=64M
set-variable=thread_cache=8
set-variable=query_cache_size=32M
set-variable=tmp_table_size=32M
set-variable=max_connections=900
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As you are on Win32 it is possible that it is a quirk related to the Win32 ports of Perl/DBI/DBD::mysql/MySQL. If you have a Linux box with MySQL it would be interesting to see if the problem is repeatable on the more native platform.

cheers

tachyon

Thanks tachyon - the new settings have fixed the problem. I'm not sure which one, I haven't played with the new settings, but I think it may have been the query_cache_size, as all queries that are run more than once run faster, also from the mysql prompt.
Still the issue remains for a query that will take longer than the prescribed 30 seconds, but whatever.
Thanks again for helping.
RC